Endocrine dysfunction and parameters of metabolic syndrome were assessed in 91 patients aged 4.3-32.5 years who underwent allogeneic or autologous BMT in childhood. Final short stature, found in five of the 35 patients who attained final height, was associated with the underlying disease (specifically, Fanconi anemia) (P ¼ 0.0013), previous cranial irradiation (P ¼ 0.0007), type of conditioning irradiation (Po0.05) and allogeneic BMT (P ¼ 0.05). Growth hormone deficiency (n ¼ 10) was associated with previous cranial irradiation (Po0.005) and conditioning total body irradiation (Po0.001). Twelve patients had primary hypothyroidism, one had hyperthyroidism and one papillary thyroid carcinoma. Hypothyroidism was associated with neck/mediastinal (Po0.005) and conditioning irradiation (Po0.05). Primary gonadal failure was found in 24 of the mature patients (62.5% females). Hypogonadism was associated with the underlying disease (especially hematological malignancies) (Po0.05), pretransplant treatment (Po0.05), irradiation conditioning (Po0.001), older age (Po0.005) and advanced pubertal stage at BMT (Po0.05). Obesity (body mass index 42 s.d.) was found in 4.4% and type II diabetes and impaired glucose tolerance in 3.3% each. Dyslipidemia was found in 27.9% of the 43 patients tested. These findings emphasize the need for long-term follow-up of endocrine and metabolic parameters in young patients after BMT in order to offer proper treatment and improve quality of life.